Pomegranate peel polyphenols prophylaxis against SARS-CoV-2 main protease by in-silico docking and molecular dynamics study

References

• Ahmed, S. A., Abdelrheem, D. A., Abd El-Mageed, H. R., Mohamed, H. S., Rahman, A. A., Elsayed, K. N., & Ahmed, S. A. (2020). Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approach for a combination therapy. Structural Chemistry, 31(6), 2391–2412. https://doi.org/10.1007/s11224-020-01586-w
   PubMed Web of Science ®Google Scholar
• Akhtar, S., Ismail, T., Fraternale, D., & Sestili, P. (2015). Pomegranate peel and peel extracts: Chemistry and food features. Food Chemistry, 174, 417–425. https://doi.org/10.1016/j.foodchem.2014.11.035
   PubMed Web of Science ®Google Scholar
• Al-Zoreky, N. S. (2009). Antimicrobial activity of pomegranate (Punica granatum L.) fruit peels. International Journal of Food Microbiology, 134(3), 244–248. https://doi.org/10.1016/j.ijfoodmicro.2009.07.002
   PubMed Web of Science ®Google Scholar
• Beck, B. R., Shin, B., Choi, Y., Park, S., & Kang, K. (2020). Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Computational and Structural Biotechnology Journal, 18, 784–790. https://doi.org/10.1016/j.csbj.2020.03.025
   PubMed Web of Science ®Google Scholar
• Brighenti, V., Groothuis, S. F., Prencipe, F. P., Amir, R., Benvenuti, S., & Pellati, F. (2017). Metabolite fingerprinting of Punica granatum L. (pomegranate) polyphenols by means of high-performance liquid chromatography with diode array and electrospray ionization-mass spectrometry detection . Journal of Chromatography. A, 1480, 20–31. https://doi.org/10.1016/j.chroma.2016.12.017
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Chang, C. K., Lo, S. C., Wang, Y. S., & Hou, M. H. (2016). Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discovery Today, 21(4), 562–572. https://doi.org/10.1016/j.drudis.2015.11.015
   PubMed Web of Science ®Google Scholar
• Chowdhury, P. (2020). In silico investigation of phytoconstituents from Indian medicinal herb 'Tinospora cordifolia (giloy)' against SARS-CoV-2 (COVID-19) by molecular dynamics approach . Journal of Biomolecular Structure & Dynamics, 18, 1–18. https://doi.org/10.1080/07391102.2020.1803968
   Google Scholar
• Das, P., Majumder, R., Mandal, M., & Basak, P. (2020). In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis. Journal of Biomolecular Structure & Dynamics, 18, 1–16. https://doi.org/10.1080/07391102.2020.1796799
   Google Scholar
• De Loof, H., Nilsson, L., & Rigler, R. (1992). Molecular dynamics simulation of galanin in aqueous and nonaqueous solution. Journal of the American Chemical Society, 114(11), 4028–4035. https://doi.org/10.1021/ja00037a002
   Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Fischer, U. A., Carle, R., & Kammerer, D. R. (2011). Identification and quantification of phenolic compounds from pomegranate (Punica granatum L.) peel, mesocarp, aril and differently produced juices by HPLC-DAD-ESI/MS(n). Food Chemistry, 127(2), 807–821. https://doi.org/10.1016/j.foodchem.2010.12.156
   PubMed Web of Science ®Google Scholar
• Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure & Dynamics, 39(12), 4313–4362. https://doi.org/10.1080/07391102.2020.1779818
   Web of Science ®Google Scholar
• Gil, M. I., Tomás-Barberán, F. A., Hess-Pierce, B., Holcroft, D. M., & Kader, A. A. (2000). Antioxidant activity of pomegranate juice and its relationship with phenolic composition and processing. Journal of Agricultural and Food Chemistry, 48(10), 4581–4589. https://doi.org/10.1021/jf000404a
   PubMed Web of Science ®Google Scholar
• Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes. Journal of Molecular Biology, 330(4), 891–913. https://doi.org/10.1016/S0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method . Molecular Informatics, 31(2), 114–122. https://doi.org/10.1002/minf.201100135
   PubMed Web of Science ®Google Scholar
• Ismail, T., Sestili, P., & Akhtar, S. (2012). Pomegranate peel and fruit extracts: A review of potential anti-inflammatory and anti-infective effects. Journal of Ethnopharmacology, 143(2), 397–405. https://doi.org/10.1016/j.jep.2012.07.004
   PubMed Web of Science ®Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors . Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Madura, J. D. (1983). Quantum and statistical mechanical studies of liquids.25. Solvation and conformation of methanol in water. Journal of the American Chemical Society, 105(6), 1407–1413. https://doi.org/10.1021/ja00344a001
   Web of Science ®Google Scholar
• Khan, M. Y., & Kumar, V. (2019). Mechanism & inhibition kinetics of bioassay-guided fractions of Indian medicinal plants and foods as ACE inhibitors. Journal of Traditional and Complementary Medicine, 9(1), 73–84. https://doi.org/10.1016/j.jtcme.2018.02.001
   PubMedGoogle Scholar
• Li, J., He, X., Li, M., Zhao, W., Liu, L., & Kong, X. (2015). Chemical fingerprint and quantitative analysis for quality control of polyphenols extracted from pomegranate peel by HPLC. Food Chemistry, 176, 7–11. https://doi.org/10.1016/j.foodchem.2014.12.040
   PubMed Web of Science ®Google Scholar
• Lu, J., Wei, Y., & Yuan, Q. (2007). Preparative separation of punicalagin from pomegranate husk by high-speed countercurrent chromatography. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, 857(1), 175–179. https://doi.org/10.1016/j.jchromb.2007.06.038
   PubMed Web of Science ®Google Scholar
• Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113–135. https://doi.org/10.1023/A:1008763014207
   Google Scholar
• Metz, A., Pfleger, C., Kopitz, H., Pfeiffer-Marek, S., Baringhaus, K.-H., & Gohlke, H. (2012). Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface. Journal of Chemical Information and Modeling, 52(1), 120–133. https://doi.org/10.1021/ci200322s
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Nosé, S. (1984). A unified formulation of the constant temperature molecular dynamics methods. The Journal of Chemical Physics, 81(1), 511–519. https://doi.org/10.1063/1.447334
   Web of Science ®Google Scholar
• Qu, W., Breksa, A. P., III, Pan, Z., & Ma, H. (2012). Quantitative determination of major polyphenol constituents in pomegranate products. Food Chemistry, 132(3), 1585–1591. https://doi.org/10.1016/j.foodchem.2011.11.106
   PubMed Web of Science ®Google Scholar
• Rajkumar, R. P. (2020). Ayurveda and COVID-19: Where psychoneuroimmunology and the meaning response meet. Brain, Behavior, and Immunity, 87, 8–9. https://doi.org/10.1016/j.bbi.2020.04.056
   PubMed Web of Science ®Google Scholar
• Rakshit, M., & Srivastav, P. P. (2021). Optimization of pulsed ultrasonic assisted extraction of punicalagin from pomegranate (Punica granatum) peel: A comparison between response surface methodology and artificial neural network‐multiobjective genetic algorithm. Journal of Food Processing and Preservation, 45(1), e15078. https://doi.org/10.1111/jfpp.15078
   Web of Science ®Google Scholar
• Rakshit, M., Srivastav, P. P., & Bhunia, K. (2020). Kinetic modeling of ultrasonic‐assisted extraction of punicalagin from pomegranate peel. Journal of Food Process Engineering, 43(11), e13533. https://doi.org/10.1111/jfpe.13533
   Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sohrabi, C., Alsafi, Z., O'Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., & Agha, R. (2020). World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19). International Journal of Surgery, 76, 71–76. https://doi.org/10.1016/j.ijsu.2020.02.034
   PubMed Web of Science ®Google Scholar
• Sundararajan, A., Ganapathy, R., Huan, L., Dunlap, J. R., Webby, R. J., Kotwal, G. J., & Sangster, M. Y. (2010). Influenza virus variation in susceptibility to inactivation by pomegranate polyphenols is determined by envelope glycoproteins. Antiviral Research, 88(1), 1–9. https://doi.org/10.1016/j.antiviral.2010.06.014
   PubMed Web of Science ®Google Scholar
• Thuy, B. T. P., My, T. T. A., Hai, N. T. T., Hieu, L. T., Hoa, T. T., Thi Phuong Loan, H., Triet, N. T., Anh, T. T. V., Quy, P. T., Tat, P. V., Hue, N. V., Quang, D. T., Trung, N. T., Tung, V. T., Huynh, L. K., & Nhung, N. T. A. (2020). Investigation into SARS-CoV-2 resistance of compounds in garlic essential oil. ACS Omega, 5(14), 8312–8320. https://doi.org/10.1021/acsomega.0c00772
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Wang, D., Hu, B., Hu, C., Zhu, F., Liu, X., Zhang, J., Wang, B., Xiang, H., Cheng, Z., Xiong, Y., Zhao, Y., Li, Y., Wang, X., & Peng, Z. (2020). Clinical characteristics of 138 hospitalized patients with 2019 novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA, 323(11), 1061–1069. https://doi.org/10.1001/jama.2020.1585
   PubMed Web of Science ®Google Scholar
• Wang, J., Morin, P., Wang, W., & Kollman, P. A. (2001). Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. Journal of the American Chemical Society, 123(22), 5221–5230. https://doi.org/10.1021/ja003834q
   PubMed Web of Science ®Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (New York, N.Y.), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar